GapMind for catabolism of small carbon sources

 

D-fructose catabolism in Escherichia coli BW25113

Best path

fruA, fruB, 1pfk, fba, tpi

Also see fitness data for the top candidates

Rules

Overview: Many bacteria take up fructose by a phosphotransferase (PTS) system that forms fructose 1-phosphate; this can be consumed via 1-phosphofructokinase and glycolysis (link). Alternatively, some PTS systems form fructose 6-phosphate, which is a central metabolic intermediate. Fructose can also be taken up directly and then phosphorylated to fructose 6-phosphate, a central metabolic intermediate. Another path is known in Aeromonas hydrophila -- phosphofructomutase converts fructose 1-phosphate (formed by a PTS system) to fructose 6-phosphate (PMID:9579084). This path is not included in GapMind because phosphofructomutase has not been linked to sequence. Also, in eukaryotes, fructose-1,6-bisphosphate aldolase is reported to cleave fructose 1-phosphate to glycerone phosphate and glyceraldehyde (link). This would make 1-phosphofructokinase unnececessary. It's not clear that this occurs in prokaryotes, so this is not listed.

37 steps (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fruA fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components b2167 b0731
fruB fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components b2169
1pfk 1-phosphofructokinase b2168 b1723
fba fructose 1,6-bisphosphate aldolase b2925 b2097
tpi triose-phosphate isomerase b3919 b2926
Alternative steps:
araS fructose ABC transporter, substrate-binding component AraS
araT fructose ABC transporter, permease component 2 (AraT)
araU fructose ABC transporter, permease component 1 (AraU)
araV fructose ABC transporter, ATPase component AraV b0262 b3450
BT1758 fructose transporter
ffz fructose facilitator (uniporter)
frcA fructose ABC transporter, ATPase component FrcA b3749 b1900
frcB fructose ABC transporter, substrate-binding component FrcB
frcC fructose ABC transporter, permease component FrcC b3750 b2148
frt1 fructose:H+ symporter Frt1 b2943 b2841
fruD fructose-specific PTS system (fructose 1-phosphate forming), EII-A component b0731
fruE fructose ABC transporter, substrate-binding component FruE b4227
fruF fructose ABC transporter, permease component 1 (FruF) b4230 b3750
fruG fructose ABC transporter, permease component 2 (FruG) b4231 b3750
fruI fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components b2416 b2829
fruII-A fructose-specific PTS system (fructose 1-phosphate forming), EII-A component b3204 b3947
fruII-ABC fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components b2167 b0731
fruII-B fructose-specific PTS system (fructose 1-phosphate forming), EII-B component b3950 b2167
fruII-C fructose-specific PTS system (fructose 1-phosphate forming), EII-C component b2167 b3949
fruK fructose ABC transporter, ATPase component FruK b4485 b3749
fruP fructose porter FruP b2801
ght6 high-affinity fructose transporter ght6
glcP fructose:H+ symporter GlcP b4031 b2943
levD fructose PTS system (fructose 6-phosphate forming), EII-A component b1817
levDE fructose PTS system (fructose 6-phosphate forming), EII-AB component b1817
levE fructose PTS system (fructose 6-phosphate forming), EII-B component b1817 b3133
levF fructose PTS system (fructose 6-phosphate forming), EII-C component b1818
levG fructose PTS system (fructose 6-phosphate forming), EII-D component b1819 b3140
scrK fructokinase b0394 b1119
Slc2a5 fructose:H+ symporter b2943 b2841
STP6 sugar transport protein 6 b2943
THT2A fructose THT2A

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory